Markus Riester
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: devel |
| git_last_commit: 75e92bb |
| git_last_commit_date: 2025-07-22 14:20:40 -0400 (Tue, 22 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-18 12:06 -0400 (Sat, 18 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1658/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.15.4 (landing page) Markus Riester
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: PureCN |
| Version: 2.15.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.4.tar.gz |
| StartedAt: 2025-10-17 21:33:07 -0400 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 21:38:55 -0400 (Fri, 17 Oct 2025) |
| EllapsedTime: 348.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.15.4’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PureCN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callAmplificationsInLowPurity 13.912 0.205 14.442
segmentationPSCBS 13.214 0.135 13.424
filterIntervals 7.249 0.195 7.557
runAbsoluteCN 5.865 0.118 6.086
segmentationHclust 5.261 0.140 5.461
annotateTargets 5.082 0.209 5.401
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.15.4’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("PureCN")
WARN [2025-10-17 21:36:36] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-10-17 21:36:36] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-10-17 21:36:40] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-10-17 21:36:41] tumor.coverage.file and interval.file do not align.
FATAL [2025-10-17 21:36:41]
FATAL [2025-10-17 21:36:41] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:41] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:36:41] Cannot find all contig lengths while exporting interval file.
INFO [2025-10-17 21:36:42] Processing seq1:1-21 (1/3)...
INFO [2025-10-17 21:36:42] Processing seq1:1227-1247 (2/3)...
INFO [2025-10-17 21:36:42] Processing seq2:594-614 (3/3)...
WARN [2025-10-17 21:36:42] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-10-17 21:36:43] Need either f or purity and ploidy.
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:36:43] f not in expected range.
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:36:43] coverage not in expected range (>=2)
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:36:43] purity not in expected range.
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:36:43] ploidy not in expected range.
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:36:43] cell.fraction not in expected range.
FATAL [2025-10-17 21:36:43]
FATAL [2025-10-17 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:36:43] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:36:44] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:36:44] You are likely not using the correct baits file!
WARN [2025-10-17 21:36:44] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:36:44] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:36:44] Processing on-target regions...
INFO [2025-10-17 21:36:44] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-17 21:36:44] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-17 21:36:44] Tumor/normal noise ratio: 19.041
WARN [2025-10-17 21:36:44] Extensive noise in tumor compared to normals.
INFO [2025-10-17 21:36:59] Tumor/normal noise ratio: 19.041
WARN [2025-10-17 21:36:59] Extensive noise in tumor compared to normals.
INFO [2025-10-17 21:37:01] Using BiocParallel for parallel optimization.
FATAL [2025-10-17 21:37:06] pvalue.cutoff not within expected range or format.
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:06] pvalue.cutoff not within expected range or format.
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:06] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:06] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:06] purity not within expected range or format.
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:06] purity not within expected range or format.
FATAL [2025-10-17 21:37:06]
FATAL [2025-10-17 21:37:06] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:06] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:07] ------------------------------------------------------------
INFO [2025-10-17 21:37:07] PureCN 2.15.4
INFO [2025-10-17 21:37:07] ------------------------------------------------------------
INFO [2025-10-17 21:37:07] Loading coverage files...
INFO [2025-10-17 21:37:07] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:07] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:07] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:07] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:07] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:37:07] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:07] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:07] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:07] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:07] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:07] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:07] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:07] Loading VCF...
INFO [2025-10-17 21:37:07] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:07] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:07] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:07] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:07] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:07] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:07] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:07] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:07] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-17 21:37:08] 1.2% of targets contain variants.
INFO [2025-10-17 21:37:08] Removing 4 variants outside intervals.
INFO [2025-10-17 21:37:08] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:37:08] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:37:08] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-10-17 21:37:08] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:37:08] Sample sex: ?
INFO [2025-10-17 21:37:08] Segmenting data...
INFO [2025-10-17 21:37:08] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:37:08] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:37:08] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:37:08] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-17 21:37:08] Using 121 variants.
INFO [2025-10-17 21:37:08] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:37:08] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:37:09] Local optima: 0.63/1.9, 0.5/2
INFO [2025-10-17 21:37:09] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-17 21:37:09] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-10-17 21:37:09] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-17 21:37:09] Fitting variants with beta model for local optimum 1/2...
INFO [2025-10-17 21:37:09] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-17 21:37:10] Optimized purity: 0.65
INFO [2025-10-17 21:37:10] Done.
INFO [2025-10-17 21:37:10] ------------------------------------------------------------
INFO [2025-10-17 21:37:10] Estimating callable regions.
FATAL [2025-10-17 21:37:11] exclude not a GRanges object.
FATAL [2025-10-17 21:37:11]
FATAL [2025-10-17 21:37:11] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:11] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:11] callable not a GRanges object.
FATAL [2025-10-17 21:37:11]
FATAL [2025-10-17 21:37:11] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:11] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:37:14] tumor.coverage.file and interval.file do not align.
INFO [2025-10-17 21:37:14] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-10-17 21:37:14] No gc_bias column in interval.file.
FATAL [2025-10-17 21:37:14]
FATAL [2025-10-17 21:37:14] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:14] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:15] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-10-17 21:37:15]
FATAL [2025-10-17 21:37:15] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:15] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:15] No reptiming column in interval.file.
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
FATAL [2025-10-17 21:37:17] Purity or Ploidy not numeric or in expected range.
FATAL [2025-10-17 21:37:17]
FATAL [2025-10-17 21:37:17] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:17] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
INFO [2025-10-17 21:37:17] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.rds...
FATAL [2025-10-17 21:37:17] 'Failed' column in
FATAL [2025-10-17 21:37:17] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284863477f6b.csv
FATAL [2025-10-17 21:37:17] not logical(1).
FATAL [2025-10-17 21:37:17]
FATAL [2025-10-17 21:37:17] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:17] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:17] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:17] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:17] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:17] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:17] Processing on-target regions...
INFO [2025-10-17 21:37:18] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-17 21:37:18] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-17 21:37:19] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:19] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:19] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:19] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:19] Processing on-target regions...
INFO [2025-10-17 21:37:19] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-17 21:37:19] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-17 21:37:20] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:20] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:20] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:20] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:20] Processing on-target regions...
INFO [2025-10-17 21:37:21] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-17 21:37:21] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-10-17 21:37:21] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:21] Sample sex: NA
WARN [2025-10-17 21:37:21] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:21] Sample sex: NA
INFO [2025-10-17 21:37:21] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:21] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:21] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:21] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-17 21:37:21] Length of normal.coverage.files and sex different
FATAL [2025-10-17 21:37:21]
FATAL [2025-10-17 21:37:21] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:21] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:37:23] Target intervals were not sorted.
INFO [2025-10-17 21:37:23] 560 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:23] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:23] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:23] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:23] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:23] Processing on-target regions...
INFO [2025-10-17 21:37:23] Removing 978 intervals with low coverage in normalDB.
INFO [2025-10-17 21:37:23] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-10-17 21:37:24] tumor.coverage.file and normalDB do not align.
FATAL [2025-10-17 21:37:24]
FATAL [2025-10-17 21:37:24] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:24] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:24] At least 2 normal.coverage.files required.
FATAL [2025-10-17 21:37:24]
FATAL [2025-10-17 21:37:24] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:24] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:25] ------------------------------------------------------------
INFO [2025-10-17 21:37:25] PureCN 2.15.4
INFO [2025-10-17 21:37:25] ------------------------------------------------------------
INFO [2025-10-17 21:37:25] Loading coverage files...
INFO [2025-10-17 21:37:25] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:25] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:25] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:25] Removing 228 intervals with missing log.ratio.
FATAL [2025-10-17 21:37:25] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-10-17 21:37:25] NormalDB.R.
FATAL [2025-10-17 21:37:25]
FATAL [2025-10-17 21:37:25] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:25] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:25] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-10-17 21:37:25] NormalDB.R.
FATAL [2025-10-17 21:37:25]
FATAL [2025-10-17 21:37:25] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:25] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:25] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-10-17 21:37:25] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-10-17 21:37:25]
FATAL [2025-10-17 21:37:25] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:25] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:25] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:25] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:25] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-17 21:37:25] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-17 21:37:25] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:25] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:25] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:25] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:25] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-17 21:37:25] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-17 21:37:26] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:26] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:26] Removing 6 blacklisted variants.
INFO [2025-10-17 21:37:26] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:26] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:26] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-17 21:37:26] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-17 21:37:26] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:26] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-10-17 21:37:26] MuTect stats file lacks contig and position columns.
INFO [2025-10-17 21:37:26] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:26] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:26] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-17 21:37:26] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-17 21:37:26] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:26] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-10-17 21:37:26] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-10-17 21:37:26] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-10-17 21:37:26] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:26] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:26] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-10-17 21:37:26] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-10-17 21:37:26] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:26] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:26] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-10-17 21:37:26] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-10-17 21:37:27] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:27] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:27] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:27] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-10-17 21:37:27] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-10-17 21:37:27] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:27] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:27] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-10-17 21:37:27] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-10-17 21:37:27] No variants passed filter BQ.
FATAL [2025-10-17 21:37:27]
FATAL [2025-10-17 21:37:27] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:27] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:27] Found 11 variants in VCF file.
WARN [2025-10-17 21:37:27] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-10-17 21:37:27] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:28] Found 11 variants in VCF file.
WARN [2025-10-17 21:37:28] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-10-17 21:37:28] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:28] Found 11 variants in VCF file.
WARN [2025-10-17 21:37:28] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-10-17 21:37:28] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:28] Found 1000 variants in VCF file.
INFO [2025-10-17 21:37:28] Removing 2 triallelic sites.
WARN [2025-10-17 21:37:28] Having trouble guessing SOMATIC status...
WARN [2025-10-17 21:37:28] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-10-17 21:37:28] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:29] Found 12 variants in VCF file.
INFO [2025-10-17 21:37:29] Removing 1 triallelic sites.
WARN [2025-10-17 21:37:29] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-10-17 21:37:29] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-10-17 21:37:29] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-17 21:37:29] BQ FORMAT field contains NAs.
INFO [2025-10-17 21:37:29] Found 2331 variants in VCF file.
INFO [2025-10-17 21:37:29] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:29] Found 2331 variants in VCF file.
INFO [2025-10-17 21:37:29] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-17 21:37:29] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-10-17 21:37:29] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:29] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-17 21:37:29] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-17 21:37:29] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:29] Found 2331 variants in VCF file.
INFO [2025-10-17 21:37:30] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-17 21:37:30] BQ FORMAT field contains NAs.
WARN [2025-10-17 21:37:30] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:30] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:30] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-10-17 21:37:30] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-10-17 21:37:30] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-10-17 21:37:30] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:30] No germline variants in VCF.
FATAL [2025-10-17 21:37:30] No solution with id hello
FATAL [2025-10-17 21:37:30]
FATAL [2025-10-17 21:37:30] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:30] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:30] No solution with id 100
FATAL [2025-10-17 21:37:30]
FATAL [2025-10-17 21:37:30] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:30] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:31] all.data and w have different lengths.
FATAL [2025-10-17 21:37:31]
FATAL [2025-10-17 21:37:31] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:31] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:31] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:31] No mappability scores provided.
WARN [2025-10-17 21:37:31] No reptiming scores provided.
INFO [2025-10-17 21:37:31] Calculating GC-content...
INFO [2025-10-17 21:37:31] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:31] No mappability scores provided.
WARN [2025-10-17 21:37:31] No reptiming scores provided.
INFO [2025-10-17 21:37:31] Calculating GC-content...
INFO [2025-10-17 21:37:31] Splitting 5 large targets to an average width of 400.
INFO [2025-10-17 21:37:31] Removing 1 targets overlapping with exclude.
WARN [2025-10-17 21:37:31] No mappability scores provided.
WARN [2025-10-17 21:37:31] No reptiming scores provided.
INFO [2025-10-17 21:37:31] Calculating GC-content...
WARN [2025-10-17 21:37:31] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:31] Splitting 5 large targets to an average width of 400.
FATAL [2025-10-17 21:37:31] off.target.padding must be negative.
FATAL [2025-10-17 21:37:31]
FATAL [2025-10-17 21:37:31] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:31] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:31] Interval coordinates should start at 1, not at 0
FATAL [2025-10-17 21:37:31]
FATAL [2025-10-17 21:37:31] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:31] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:37:32] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
FATAL [2025-10-17 21:37:32] No off-target regions after filtering for mappability and
FATAL [2025-10-17 21:37:32] off.target.padding
FATAL [2025-10-17 21:37:32]
FATAL [2025-10-17 21:37:32] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:32] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:37:32] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:32] No mappability scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
WARN [2025-10-17 21:37:32] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:32] Averaging reptiming into bins of size 200...
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:32] No mappability scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
WARN [2025-10-17 21:37:32] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:32] Splitting 6 large targets to an average width of 200.
WARN [2025-10-17 21:37:32] No mappability scores provided.
WARN [2025-10-17 21:37:32] No reptiming scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
WARN [2025-10-17 21:37:32] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:32] No mappability scores provided.
WARN [2025-10-17 21:37:32] No reptiming scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
INFO [2025-10-17 21:37:32] Tiling off-target regions to an average width of 200000.
WARN [2025-10-17 21:37:32] No mappability scores provided.
WARN [2025-10-17 21:37:32] No reptiming scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
WARN [2025-10-17 21:37:32] Intervals contain off-target regions. Will not change intervals.
WARN [2025-10-17 21:37:32] No mappability scores provided.
WARN [2025-10-17 21:37:32] No reptiming scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
INFO [2025-10-17 21:37:32] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:32] No reptiming scores provided.
INFO [2025-10-17 21:37:32] Calculating GC-content...
WARN [2025-10-17 21:37:33] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:33] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:33] No reptiming scores provided.
INFO [2025-10-17 21:37:33] Calculating GC-content...
WARN [2025-10-17 21:37:33] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:33] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:33] 1 intervals without mappability score (1 on-target).
INFO [2025-10-17 21:37:33] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-10-17 21:37:33] No reptiming scores provided.
INFO [2025-10-17 21:37:33] Calculating GC-content...
WARN [2025-10-17 21:37:33] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-17 21:37:33] Splitting 5 large targets to an average width of 400.
INFO [2025-10-17 21:37:33] Tiling off-target regions to an average width of 200000.
WARN [2025-10-17 21:37:33] No reptiming scores provided.
INFO [2025-10-17 21:37:33] Calculating GC-content...
INFO [2025-10-17 21:37:33] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:33] No mappability scores provided.
WARN [2025-10-17 21:37:33] No reptiming scores provided.
INFO [2025-10-17 21:37:33] Calculating GC-content...
WARN [2025-10-17 21:37:33] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-10-17 21:37:33] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:33] No mappability scores provided.
WARN [2025-10-17 21:37:33] No reptiming scores provided.
INFO [2025-10-17 21:37:33] Calculating GC-content...
FATAL [2025-10-17 21:37:34] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-10-17 21:37:34]
FATAL [2025-10-17 21:37:34] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:34] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:37:34] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-10-17 21:37:34] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-10-17 21:37:34] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:34] No reptiming scores provided.
INFO [2025-10-17 21:37:34] Calculating GC-content...
WARN [2025-10-17 21:37:34] Found small target regions (< 60bp). Will resize them.
INFO [2025-10-17 21:37:34] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:34] No mappability scores provided.
WARN [2025-10-17 21:37:34] No reptiming scores provided.
INFO [2025-10-17 21:37:34] Calculating GC-content...
WARN [2025-10-17 21:37:34] Found small target regions (< 60bp). Will drop them.
INFO [2025-10-17 21:37:34] Splitting 4 large targets to an average width of 400.
WARN [2025-10-17 21:37:34] No mappability scores provided.
WARN [2025-10-17 21:37:34] No reptiming scores provided.
INFO [2025-10-17 21:37:34] Calculating GC-content...
WARN [2025-10-17 21:37:34] Found small target regions (< 200bp). Will resize them.
INFO [2025-10-17 21:37:34] Splitting 5 large targets to an average width of 400.
WARN [2025-10-17 21:37:34] No mappability scores provided.
WARN [2025-10-17 21:37:34] No reptiming scores provided.
INFO [2025-10-17 21:37:34] Calculating GC-content...
INFO [2025-10-17 21:37:34] Found 20 variants in VCF file.
INFO [2025-10-17 21:37:34] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-17 21:37:34] Did not find base quality scores, will use global error rate of 0.0010 instead.
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
FATAL [2025-10-17 21:37:34] Error reading AllelicCountsFile
FATAL [2025-10-17 21:37:34] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-10-17 21:37:34]
FATAL [2025-10-17 21:37:34] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:34] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:34] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:34] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-17 21:37:34] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-10-17 21:37:35] ------------------------------------------------------------
INFO [2025-10-17 21:37:35] PureCN 2.15.4
INFO [2025-10-17 21:37:35] ------------------------------------------------------------
INFO [2025-10-17 21:37:35] Loading coverage files...
INFO [2025-10-17 21:37:35] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:35] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:35] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:35] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:35] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:37:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:35] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:35] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:35] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:35] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:35] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:35] Loading VCF...
INFO [2025-10-17 21:37:35] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:35] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:35] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:35] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:35] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:35] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:35] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:35] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-17 21:37:35] 1.2% of targets contain variants.
INFO [2025-10-17 21:37:35] Removing 4 variants outside intervals.
INFO [2025-10-17 21:37:35] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:37:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:37:35] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-10-17 21:37:35] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:37:35] Sample sex: ?
INFO [2025-10-17 21:37:35] Segmenting data...
INFO [2025-10-17 21:37:35] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:37:35] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:37:36] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:37:36] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-17 21:37:36] Using 121 variants.
INFO [2025-10-17 21:37:36] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:37:36] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:37:36] Local optima: 0.65/1.8, 0.52/2
INFO [2025-10-17 21:37:36] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-17 21:37:36] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-10-17 21:37:36] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-17 21:37:36] Fitting variants with beta model for local optimum 1/2...
INFO [2025-10-17 21:37:36] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-17 21:37:37] Optimized purity: 0.65
INFO [2025-10-17 21:37:37] Done.
INFO [2025-10-17 21:37:37] ------------------------------------------------------------
FATAL [2025-10-17 21:37:38] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-10-17 21:37:38]
FATAL [2025-10-17 21:37:38] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-10-17 21:37:38] Please report bug (PureCN 2.15.4).
INFO [2025-10-17 21:37:38] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-10-17 21:37:38] Re-centering provided segment means (offset -0.0033).
INFO [2025-10-17 21:37:38] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-10-17 21:37:38] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-10-17 21:37:38] Re-centering provided segment means (offset -0.0037).
INFO [2025-10-17 21:37:38] 576 on-target bins with low coverage in all samples.
WARN [2025-10-17 21:37:38] You are likely not using the correct baits file!
WARN [2025-10-17 21:37:38] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:38] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:38] Processing on-target regions...
INFO [2025-10-17 21:37:38] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-17 21:37:38] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-17 21:37:39] ------------------------------------------------------------
INFO [2025-10-17 21:37:39] PureCN 2.15.4
INFO [2025-10-17 21:37:39] ------------------------------------------------------------
INFO [2025-10-17 21:37:39] Using BiocParallel for parallel optimization.
INFO [2025-10-17 21:37:39] Loading coverage files...
INFO [2025-10-17 21:37:39] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:39] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:39] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:39] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:39] Removing 705 intervals excluded in normalDB.
INFO [2025-10-17 21:37:39] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-10-17 21:37:39] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:39] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:39] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:39] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:39] Sample sex: ?
INFO [2025-10-17 21:37:39] Segmenting data...
INFO [2025-10-17 21:37:39] Interval weights found, will use weighted CBS.
INFO [2025-10-17 21:37:39] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:37:39] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-10-17 21:37:40] Found 52 segments with median size of 29.35Mb.
INFO [2025-10-17 21:37:40] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:37:40] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:37:40] Local optima: 0.65/1.8, 0.52/2
INFO [2025-10-17 21:37:41] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-17 21:37:41] Done.
INFO [2025-10-17 21:37:41] ------------------------------------------------------------
INFO [2025-10-17 21:37:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file284837f2c6d4.rds...
FATAL [2025-10-17 21:37:41] runAbsoluteCN was run without a VCF file.
FATAL [2025-10-17 21:37:41]
FATAL [2025-10-17 21:37:41] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:41] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:37:41] runAbsoluteCN was run without a VCF file.
FATAL [2025-10-17 21:37:41]
FATAL [2025-10-17 21:37:41] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:41] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:41] ------------------------------------------------------------
INFO [2025-10-17 21:37:41] PureCN 2.15.4
INFO [2025-10-17 21:37:41] ------------------------------------------------------------
INFO [2025-10-17 21:37:41] Loading coverage files...
INFO [2025-10-17 21:37:41] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:41] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:41] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:41] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:41] Removing 705 intervals excluded in normalDB.
INFO [2025-10-17 21:37:41] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-10-17 21:37:41] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:41] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:41] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:41] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:41] Sample sex: ?
INFO [2025-10-17 21:37:41] Segmenting data...
INFO [2025-10-17 21:37:41] Interval weights found, will use weighted PSCBS.
FATAL [2025-10-17 21:37:41] segmentationPSCBS requires VCF file.
FATAL [2025-10-17 21:37:41]
FATAL [2025-10-17 21:37:41] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:41] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:43] ------------------------------------------------------------
INFO [2025-10-17 21:37:43] PureCN 2.15.4
INFO [2025-10-17 21:37:43] ------------------------------------------------------------
INFO [2025-10-17 21:37:43] Loading coverage files...
FATAL [2025-10-17 21:37:44] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] min.ploidy or max.ploidy not within expected range.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] min.ploidy or max.ploidy not within expected range.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] test.num.copy not within expected range.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
WARN [2025-10-17 21:37:44] test.num.copy outside recommended range.
FATAL [2025-10-17 21:37:44] max.non.clonal not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
WARN [2025-10-17 21:37:44] test.num.copy outside recommended range.
FATAL [2025-10-17 21:37:44] max.non.clonal not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] test.purity not within expected range.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] Loading coverage files...
FATAL [2025-10-17 21:37:44] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-10-17 21:37:44] and I'm stopping here.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] Loading coverage files...
FATAL [2025-10-17 21:37:44] Length of log.ratio different from tumor coverage.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] prior.purity must have the same length as test.purity.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] min.gof not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] prior.purity not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] prior.purity must add to 1. Sum is 1.5
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] max.homozygous.loss not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] prior.K not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] prior.contamination not within expected range or format.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] Iterations not in the expected range from 10 to 250.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
FATAL [2025-10-17 21:37:44] Iterations not in the expected range from 10 to 250.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] Loading coverage files...
FATAL [2025-10-17 21:37:44] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-10-17 21:37:44] interval.file.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] PureCN 2.15.4
INFO [2025-10-17 21:37:44] ------------------------------------------------------------
INFO [2025-10-17 21:37:44] Loading coverage files...
FATAL [2025-10-17 21:37:44] Interval files in normal and tumor different.
FATAL [2025-10-17 21:37:44]
FATAL [2025-10-17 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:44] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] PureCN 2.15.4
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] Loading coverage files...
INFO [2025-10-17 21:37:45] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-10-17 21:37:45] Large difference in coverage of tumor and normal.
FATAL [2025-10-17 21:37:45] No finite intervals.
FATAL [2025-10-17 21:37:45]
FATAL [2025-10-17 21:37:45] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:45] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] PureCN 2.15.4
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] Loading coverage files...
INFO [2025-10-17 21:37:45] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:45] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:45] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:45] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:45] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:37:45] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:45] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:45] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:45] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:45] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:45] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:45] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:45] Loading VCF...
INFO [2025-10-17 21:37:45] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:45] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:45] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:45] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:45] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:45] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:45] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:45] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:45] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) :
Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In UseMethod("sort") :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpiKdIsA/file28486067a19b.tsv)
3: In UseMethod("sort") :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-10-17 21:37:45] Could not import snp.blacklist
FATAL [2025-10-17 21:37:45] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-10-17 21:37:45] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-10-17 21:37:45] unsupported
FATAL [2025-10-17 21:37:45]
FATAL [2025-10-17 21:37:45] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:37:45] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] PureCN 2.15.4
INFO [2025-10-17 21:37:45] ------------------------------------------------------------
INFO [2025-10-17 21:37:45] Loading coverage files...
INFO [2025-10-17 21:37:46] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:46] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:46] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:46] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:46] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:37:46] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:46] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:46] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:46] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-10-17 21:37:46] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:46] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:46] Loading VCF...
INFO [2025-10-17 21:37:46] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:46] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:46] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:46] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:46] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:46] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:46] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:46] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:46] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-10-17 21:37:46] 1.0% of targets contain variants.
INFO [2025-10-17 21:37:46] Removing 2 variants outside intervals.
INFO [2025-10-17 21:37:46] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:37:46] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:37:46] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-10-17 21:37:46] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:37:46] Sample sex: ?
INFO [2025-10-17 21:37:46] Segmenting data...
INFO [2025-10-17 21:37:46] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:37:46] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:37:47] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:37:47] Found 54 segments with median size of 24.88Mb.
INFO [2025-10-17 21:37:47] Using 123 variants.
INFO [2025-10-17 21:37:47] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-10-17 21:37:47] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:37:47] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-10-17 21:37:47] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-10-17 21:37:48] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:48] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:48] Recalibrating log-ratios...
INFO [2025-10-17 21:37:48] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:48] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-17 21:37:48] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-10-17 21:37:48] Fitting variants with beta model for local optimum 1/3...
INFO [2025-10-17 21:37:48] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-10-17 21:37:49] Optimized purity: 0.65
INFO [2025-10-17 21:37:49] Done.
INFO [2025-10-17 21:37:49] ------------------------------------------------------------
INFO [2025-10-17 21:37:49] ------------------------------------------------------------
INFO [2025-10-17 21:37:49] PureCN 2.15.4
INFO [2025-10-17 21:37:49] ------------------------------------------------------------
INFO [2025-10-17 21:37:49] Loading coverage files...
INFO [2025-10-17 21:37:50] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:50] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:50] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:50] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:37:50] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:50] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:50] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:50] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:50] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:37:50] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:50] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:37:50] Loading VCF...
INFO [2025-10-17 21:37:50] Found 127 variants in VCF file.
WARN [2025-10-17 21:37:50] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-10-17 21:37:50] DB INFO flag contains NAs
INFO [2025-10-17 21:37:50] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:50] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:50] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:50] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:50] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:50] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:50] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:50] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-17 21:37:50] 1.2% of targets contain variants.
INFO [2025-10-17 21:37:50] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-10-17 21:37:50] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:37:50] Sample sex: ?
INFO [2025-10-17 21:37:50] Segmenting data...
INFO [2025-10-17 21:37:50] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:37:50] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-10-17 21:37:51] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:37:51] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-17 21:37:51] Using 123 variants.
INFO [2025-10-17 21:37:51] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:37:51] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:37:51] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-10-17 21:37:51] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-10-17 21:37:51] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-17 21:37:52] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:52] Recalibrating log-ratios...
INFO [2025-10-17 21:37:52] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-17 21:37:52] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-10-17 21:37:52] Fitting variants with beta model for local optimum 1/3...
INFO [2025-10-17 21:37:52] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-17 21:37:53] Optimized purity: 0.65
INFO [2025-10-17 21:37:53] Done.
INFO [2025-10-17 21:37:53] ------------------------------------------------------------
INFO [2025-10-17 21:37:53] ------------------------------------------------------------
INFO [2025-10-17 21:37:53] PureCN 2.15.4
INFO [2025-10-17 21:37:53] ------------------------------------------------------------
INFO [2025-10-17 21:37:53] Loading coverage files...
INFO [2025-10-17 21:37:54] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:37:54] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:37:54] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:37:54] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-10-17 21:37:54] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:37:54] Removing 15 low/high GC targets.
INFO [2025-10-17 21:37:54] Removing 21 small (< 5bp) intervals.
INFO [2025-10-17 21:37:54] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:37:54] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:37:54] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:37:54] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:37:54] Removing 36 low mappability intervals.
INFO [2025-10-17 21:37:54] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-17 21:37:54] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:37:54] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-17 21:37:54] Loading VCF...
INFO [2025-10-17 21:37:54] Found 127 variants in VCF file.
INFO [2025-10-17 21:37:54] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:37:54] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:37:54] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:37:54] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:37:54] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:37:54] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:37:54] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:37:54] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:37:54] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-17 21:37:54] 1.2% of targets contain variants.
INFO [2025-10-17 21:37:54] Removing 11 variants outside intervals.
INFO [2025-10-17 21:37:54] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:37:54] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:37:54] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-17 21:37:54] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:37:54] Sample sex: ?
INFO [2025-10-17 21:37:54] Segmenting data...
INFO [2025-10-17 21:37:54] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-10-17 21:37:54] Using unweighted PSCBS.
INFO [2025-10-17 21:37:54] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:38:05] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:38:05] Found 72 segments with median size of 27.25Mb.
INFO [2025-10-17 21:38:05] Using 114 variants.
INFO [2025-10-17 21:38:05] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:38:05] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:38:05] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-10-17 21:38:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-17 21:38:05] Recalibrating log-ratios...
INFO [2025-10-17 21:38:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-17 21:38:05] Recalibrating log-ratios...
INFO [2025-10-17 21:38:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-17 21:38:05] Recalibrating log-ratios...
INFO [2025-10-17 21:38:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-17 21:38:05] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-10-17 21:38:06] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-10-17 21:38:06] Fitting variants with beta model for local optimum 2/2...
INFO [2025-10-17 21:38:06] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-10-17 21:38:07] Optimized purity: 0.40
INFO [2025-10-17 21:38:07] Done.
INFO [2025-10-17 21:38:07] ------------------------------------------------------------
FATAL [2025-10-17 21:38:07] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-10-17 21:38:07] containing gene symbols to the interval.file.
FATAL [2025-10-17 21:38:07]
FATAL [2025-10-17 21:38:07] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:07] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] PureCN 2.15.4
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] Loading coverage files...
INFO [2025-10-17 21:38:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:38:08] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:38:08] Removing 22 small (< 5bp) intervals.
INFO [2025-10-17 21:38:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:38:08] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:38:08] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:38:08] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:38:08] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-17 21:38:08] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:38:08] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-17 21:38:08] Loading VCF...
INFO [2025-10-17 21:38:08] Found 127 variants in VCF file.
INFO [2025-10-17 21:38:08] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-10-17 21:38:08] Different chromosome names in coverage and VCF.
FATAL [2025-10-17 21:38:08]
FATAL [2025-10-17 21:38:08] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:08] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] PureCN 2.15.4
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] Loading coverage files...
INFO [2025-10-17 21:38:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-17 21:38:08] tumor.coverage.file and interval.file do not align.
FATAL [2025-10-17 21:38:08]
FATAL [2025-10-17 21:38:08] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:08] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] PureCN 2.15.4
INFO [2025-10-17 21:38:08] ------------------------------------------------------------
INFO [2025-10-17 21:38:08] Loading coverage files...
INFO [2025-10-17 21:38:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:08] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:38:09] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:38:09] Removing 15 low/high GC targets.
INFO [2025-10-17 21:38:09] Removing 21 small (< 5bp) intervals.
INFO [2025-10-17 21:38:09] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:38:09] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:38:09] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:38:09] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:38:09] Removing 36 low mappability intervals.
INFO [2025-10-17 21:38:09] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-17 21:38:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:38:09] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-17 21:38:09] Loading VCF...
INFO [2025-10-17 21:38:09] Found 127 variants in VCF file.
INFO [2025-10-17 21:38:09] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:38:09] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:38:09] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:38:09] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:38:09] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:38:09] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:38:09] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:38:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:38:09] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-17 21:38:09] 1.2% of targets contain variants.
INFO [2025-10-17 21:38:09] Removing 11 variants outside intervals.
INFO [2025-10-17 21:38:09] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:38:09] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:38:09] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-17 21:38:09] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:38:09] Sample sex: ?
INFO [2025-10-17 21:38:09] Segmenting data...
INFO [2025-10-17 21:38:09] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:38:09] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:38:10] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:38:10] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-17 21:38:10] Using 114 variants.
INFO [2025-10-17 21:38:10] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:38:10] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:38:10] Local optima: 0.63/1.9
INFO [2025-10-17 21:38:10] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-17 21:38:10] Fitting variants with beta model for local optimum 1/1...
INFO [2025-10-17 21:38:10] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-17 21:38:11] Optimized purity: 0.65
INFO [2025-10-17 21:38:11] Done.
INFO [2025-10-17 21:38:11] ------------------------------------------------------------
INFO [2025-10-17 21:38:11] ------------------------------------------------------------
INFO [2025-10-17 21:38:11] PureCN 2.15.4
INFO [2025-10-17 21:38:11] ------------------------------------------------------------
INFO [2025-10-17 21:38:11] Loading coverage files...
INFO [2025-10-17 21:38:11] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-17 21:38:11] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:11] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:38:12] Removing 228 intervals with missing log.ratio.
INFO [2025-10-17 21:38:12] Removing 15 low/high GC targets.
INFO [2025-10-17 21:38:12] Removing 21 small (< 5bp) intervals.
INFO [2025-10-17 21:38:12] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-17 21:38:12] No normalDB provided. Provide one for better results.
INFO [2025-10-17 21:38:12] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-17 21:38:12] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-17 21:38:12] Removing 36 low mappability intervals.
INFO [2025-10-17 21:38:12] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-17 21:38:12] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:38:12] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-17 21:38:12] Loading VCF...
INFO [2025-10-17 21:38:12] Found 127 variants in VCF file.
INFO [2025-10-17 21:38:12] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:38:12] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:38:12] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:38:12] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:38:12] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:38:12] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:38:12] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:38:12] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:38:12] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-17 21:38:12] 1.2% of targets contain variants.
INFO [2025-10-17 21:38:12] Removing 11 variants outside intervals.
INFO [2025-10-17 21:38:12] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:38:12] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:38:12] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-17 21:38:12] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:38:12] Sample sex: ?
INFO [2025-10-17 21:38:12] Segmenting data...
INFO [2025-10-17 21:38:12] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:38:12] Setting undo.SD parameter to 1.000000.
INFO [2025-10-17 21:38:13] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:38:13] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-17 21:38:13] Using 114 variants.
INFO [2025-10-17 21:38:13] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-17 21:38:13] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:38:13] Local optima: 0.63/1.9
INFO [2025-10-17 21:38:13] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-17 21:38:13] Fitting variants with beta model for local optimum 1/1...
WARN [2025-10-17 21:38:13] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-10-17 21:38:13] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-17 21:38:14] Optimized purity: 0.65
INFO [2025-10-17 21:38:14] Done.
INFO [2025-10-17 21:38:14] ------------------------------------------------------------
FATAL [2025-10-17 21:38:14] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-10-17 21:38:14] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-10-17 21:38:14]
FATAL [2025-10-17 21:38:14] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:14] parameters (PureCN 2.15.4).
INFO [2025-10-17 21:38:14] ------------------------------------------------------------
INFO [2025-10-17 21:38:14] PureCN 2.15.4
INFO [2025-10-17 21:38:14] ------------------------------------------------------------
INFO [2025-10-17 21:38:14] Loading coverage files...
WARN [2025-10-17 21:38:14] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-10-17 21:38:14] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:14] Allosome coverage missing, cannot determine sex.
INFO [2025-10-17 21:38:15] Removing 10 intervals with missing log.ratio.
INFO [2025-10-17 21:38:15] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-10-17 21:38:15] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-17 21:38:15] Loading VCF...
INFO [2025-10-17 21:38:15] Found 127 variants in VCF file.
INFO [2025-10-17 21:38:15] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-17 21:38:15] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-17 21:38:15] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-17 21:38:15] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-17 21:38:15] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-17 21:38:15] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-17 21:38:15] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-17 21:38:15] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-17 21:38:15] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-10-17 21:38:15] 1.0% of targets contain variants.
INFO [2025-10-17 21:38:15] Removing 0 variants outside intervals.
INFO [2025-10-17 21:38:15] Found SOMATIC annotation in VCF.
INFO [2025-10-17 21:38:15] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-17 21:38:15] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-10-17 21:38:15] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-17 21:38:15] Sample sex: ?
INFO [2025-10-17 21:38:15] Segmenting data...
INFO [2025-10-17 21:38:15] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-10-17 21:38:15] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-10-17 21:38:15] Re-centering provided segment means (offset -0.0033).
INFO [2025-10-17 21:38:15] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-17 21:38:15] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-10-17 21:38:15] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-17 21:38:15] Found 54 segments with median size of 24.88Mb.
INFO [2025-10-17 21:38:15] Using 125 variants.
INFO [2025-10-17 21:38:15] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-10-17 21:38:15] 2D-grid search of purity and ploidy...
INFO [2025-10-17 21:38:16] Local optima: 0.6/1.9
INFO [2025-10-17 21:38:16] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-10-17 21:38:16] Fitting variants with beta model for local optimum 1/1...
INFO [2025-10-17 21:38:16] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-10-17 21:38:17] Optimized purity: 0.65
INFO [2025-10-17 21:38:17] Done.
INFO [2025-10-17 21:38:17] ------------------------------------------------------------
WARN [2025-10-17 21:38:17] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:17] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-10-17 21:38:20] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-10-17 21:38:20] num.mark, seg.mean
FATAL [2025-10-17 21:38:20]
FATAL [2025-10-17 21:38:20] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:20] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:20] seg.file contains multiple samples and sampleid missing.
FATAL [2025-10-17 21:38:20]
FATAL [2025-10-17 21:38:20] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:20] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:20] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-10-17 21:38:20]
FATAL [2025-10-17 21:38:20] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:20] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:38:20] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:20] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:23] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:23] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:23] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-10-17 21:38:24] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:24] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:24] No normalDB provided. Provide one for better results.
WARN [2025-10-17 21:38:27] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:27] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:28] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-10-17 21:38:31] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:31] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:31] No normalDB provided. Provide one for better results.
WARN [2025-10-17 21:38:31] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-10-17 21:38:33] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:33] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-17 21:38:33] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-10-17 21:38:33] create one.
FATAL [2025-10-17 21:38:33]
FATAL [2025-10-17 21:38:33] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:33] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:38:33] You are likely not using the correct baits file!
WARN [2025-10-17 21:38:33] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:33] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:34] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-17 21:38:34] normalDB appears to be empty.
FATAL [2025-10-17 21:38:34]
FATAL [2025-10-17 21:38:34] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:34] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:38:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:35] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-10-17 21:38:38] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:38] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-17 21:38:38] Seqlevels missing in provided segmentation: 6
FATAL [2025-10-17 21:38:38]
FATAL [2025-10-17 21:38:38] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:38] parameters (PureCN 2.15.4).
sh: gatk: command not found
WARN [2025-10-17 21:38:39] Cannot find gatk binary in path.
WARN [2025-10-17 21:38:39] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:39] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:39] No normalDB provided. Provide one for better results.
FATAL [2025-10-17 21:38:39] segmentationHclust requires an input segmentation.
FATAL [2025-10-17 21:38:39]
FATAL [2025-10-17 21:38:39] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:39] parameters (PureCN 2.15.4).
WARN [2025-10-17 21:38:39] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:39] Allosome coverage missing, cannot determine sex.
WARN [2025-10-17 21:38:39] No normalDB provided. Provide one for better results.
FATAL [2025-10-17 21:38:48] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-10-17 21:38:48]
FATAL [2025-10-17 21:38:48] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:48] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:48] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-10-17 21:38:48]
FATAL [2025-10-17 21:38:48] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:48] parameters (PureCN 2.15.4).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-10-17 21:38:49] min.normals (0) must be >= 1.
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-10-17 21:38:49] min.normals.betafit (7).
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] min.normals.betafit (20) cannot be larger than
FATAL [2025-10-17 21:38:49] min.normals.position.specific.fit (10).
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] min.betafit.rho not within expected range or format.
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] max.betafit.rho not within expected range or format.
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
FATAL [2025-10-17 21:38:49] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-10-17 21:38:49]
FATAL [2025-10-17 21:38:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-17 21:38:49] parameters (PureCN 2.15.4).
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
>
> proc.time()
user system elapsed
149.943 5.638 145.195
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.869 | 0.014 | 0.891 | |
| annotateTargets | 5.082 | 0.209 | 5.401 | |
| bootstrapResults | 0.217 | 0.022 | 0.250 | |
| calculateBamCoverageByInterval | 0.072 | 0.005 | 0.082 | |
| calculateLogRatio | 0.345 | 0.020 | 0.377 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.685 | 0.024 | 0.779 | |
| calculatePowerDetectSomatic | 0.588 | 0.017 | 0.646 | |
| calculateTangentNormal | 1.342 | 0.027 | 1.485 | |
| callAlterations | 0.057 | 0.003 | 0.085 | |
| callAlterationsFromSegmentation | 0.607 | 0.013 | 0.732 | |
| callAmplificationsInLowPurity | 13.912 | 0.205 | 14.442 | |
| callCIN | 0.085 | 0.002 | 0.087 | |
| callLOH | 0.086 | 0.004 | 0.093 | |
| callMutationBurden | 0.565 | 0.017 | 0.598 | |
| centromeres | 0.000 | 0.001 | 0.001 | |
| correctCoverageBias | 0.582 | 0.020 | 0.625 | |
| createCurationFile | 0.151 | 0.004 | 0.162 | |
| createNormalDatabase | 0.858 | 0.016 | 0.900 | |
| filterIntervals | 7.249 | 0.195 | 7.557 | |
| filterVcfBasic | 0.219 | 0.003 | 0.223 | |
| filterVcfMuTect | 0.241 | 0.004 | 0.244 | |
| filterVcfMuTect2 | 0.209 | 0.005 | 0.215 | |
| findFocal | 3.680 | 0.035 | 3.740 | |
| findHighQualitySNPs | 0.563 | 0.006 | 0.582 | |
| getSexFromCoverage | 0.095 | 0.005 | 0.100 | |
| getSexFromVcf | 0.097 | 0.003 | 0.102 | |
| plotAbs | 0.090 | 0.003 | 0.095 | |
| poolCoverage | 0.229 | 0.013 | 0.243 | |
| predictSomatic | 0.163 | 0.002 | 0.164 | |
| preprocessIntervals | 0.220 | 0.003 | 0.227 | |
| processMultipleSamples | 0.897 | 0.018 | 0.941 | |
| readAllelicCountsFile | 0.191 | 0.001 | 0.197 | |
| readCoverageFile | 0.114 | 0.005 | 0.121 | |
| readCurationFile | 0.089 | 0.003 | 0.095 | |
| readIntervalFile | 0.058 | 0.002 | 0.061 | |
| readLogRatioFile | 0.010 | 0.001 | 0.011 | |
| readSegmentationFile | 0.003 | 0.000 | 0.004 | |
| runAbsoluteCN | 5.865 | 0.118 | 6.086 | |
| segmentationCBS | 2.795 | 0.022 | 2.833 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.002 | |
| segmentationHclust | 5.261 | 0.140 | 5.461 | |
| segmentationPSCBS | 13.214 | 0.135 | 13.424 | |
| setMappingBiasVcf | 0.124 | 0.002 | 0.125 | |
| setPriorVcf | 0.095 | 0.004 | 0.098 | |